Luca Jovine

Feature request: retain model ensembling as an option, for molecular replacement usage purposes

8

Hello, Although it is true that in most cases the 5/25 models generated by AF2 monomer/multimer are very similar to each other, we consistently find that - when using these...

Multimer predictions degraded after updating from 2.2.3 to 2.2.4?

30

Hello, this is ranking_debug.json from a test multimer run that I had performed with version 2.2.3: `{ "iptm+ptm": { "model_1_multimer_v2_pred_0": 0.8584136076107545, "model_2_multimer_v2_pred_0": 0.8055674020453231, "model_3_multimer_v2_pred_0": 0.6845710872128711, "model_4_multimer_v2_pred_0": 0.8423123043127994, "model_5_multimer_v2_pred_0": 0.8676285262204777 },...

I guess the subject says it all! But really, I think this would be a simple but useful tweak to have, which would make things much easier when one is...

Version number?

2

I have a simple question: how do I find out which version of OpenFold has been installed (by third parties) on a machine?

Endless "[Perf]: MatMul reference implementation being executed generated" messages and dramatic inference slowdown upon updating to docker 27.3.1

2

Hello, One of my systems, running Ubuntu 22.04, updated docker to version 27.3.1 (build ce12230)... after which running AlphaFold2 produces a neverending series of messages like the following once it...